There's a theme I've noticed with the show Eureka. There are some good high-concept sci-fi ideas, like what if someone could manipulate memory? And those ideas are done well, except for a B-plot that is horribly written, and eventually a 3rd act that ruins the setup.
In the case of this episode, we have the situation I described above - a man who is capable of messing with people's memory. This man has the girl of his dreams, a fancy car, and is seen as a hero in Global Dynamics, and it's very clear to the viewer he did not legitimately earn all of these accolades.
The problem starts with the B plot. The B plot centers on a character we've never met before, but who holds extreme importance to a main character. However, because the audience has no connection to this newcomer, we don't feel the same way the characters do.
These two had a history, and it's quickly made clear that the reason their history didn't live up to its potential is because it was stolen from them. But it doesn't really make sense, unless the bad guy was the clingiest 3rd wheel in history.
If the writers did not try too hard to be "good writers" and tie everything in the episode into a nice little bow, they might have had a great episode. Unfortunately, they did try too hard, and this is what we got.